Mock exam Flashcards
what are the organelles surrounded by a lipid membrane
- nucleus
- endoplasmic reticulum
- golgi apparatus
- mitochondria
what is the difference between cytosol and cytoplasm?
cytosol: fluid contained within the cytoplasm
cytoplasm: entire content within the cell membrane except the nucleus
elaborate on the asymmetry of the plasma membrane
- composition of membrane leaflets is highly uneven
- maintained by flippases and floppases
- extracellular leaflet: phosphatidylcholine, SM, phosphatidylserine, phosphatidylethanolamine
- CHL resides in cytoplasmic leaflet
- asymmetry creates a difference in orientation and positioning of proteins
- difference in lipids/protein/carb composition
what types of lipids and proteins are found in plasma membrane?
lipids: glycolipids/cholesterol/phospholipids
proteins: intrinsic (integral) /extrinsic (peripheral)
classify plasma membrane proteins based on their function
- structural proteins
- enzymes
- transport proteins
what is endocytosis and what are the different endocytic pathways?
endocytosis: process by which cells take in substances from outside of the cell by engulfing them in a vesicle
endocytic pathways
- pinocytosis
- receptor mediated endocytosis
- phagocytosis
what’s the difference between each endocytic pathway?
phagocytosis: engulfment of large particles that pinch off from the membrane to form a vacuole that surrouds the particle
receptor mediated endocytosis: ligands bind to cell surface receptors on membrane
pinocytosis: small vesicles dissolve small material in liquid
what are the general steps of phagocytosis?
- engulfment
- phagosome formation
- phagolysosome digestion
- expulsion of undigested material
what cells are capable of phagocytosis?
- neutrophils
- monocytes
- dendritic cells
- macrophages
- mast cells
what enzymes are found in lysosomes?
hydrolytic enzymes
e.g. proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, sulfatases
what is the role of iron in cells?
- electron transport chain of the mitochondria depends on iron as an electron acceptor/donor
- many enzymes of electron transport chain are iron dependent (cytochrome c/cytochrome oxidase/succinate dehydrogenase)
- it helps oxygenate blood cells and haemoglobin by binding oxygen thus aiding oxygen transport to tissues
what genes are critical for cancer?
oncogenes
tumor suppressor genes
what are apolipoproteins and what do they do?
proteins that bind lipids to form lipoproteins
they transport lipids in blood, CSF, and lymph
what diseases are caused by apolipoproteins?
- alzeheimer → amyloid beta peptide (APO E)
- parkinson’s → alpha synuclein (APO D)
- spongiform encephalopathies → prion proteins (APO E)
- familial amyloiditic polyneuropathy → transthyretin (APO A)
- huntington’s → polyQ
- familial amyotrophic lateral sclerosis → superoxide dismutase 1
define autophagy
destruction of damaged cellular components occuring in vacuoles within the cell
what is the role of the cytoskeleton in membrane traffic?
provides support and directionality
compare and contrast:
prokaryotes and eukaryotes
compare and contrast:
gram negative and gram positive bacteria
what are the different bacterial structures and what are their functions?
- pili → genetic exchange (conjugation)
- fimbrae → adhesins (attachment)/biofilm formation/hemagglutination
- flagella → motor movement/flagellin protein
- S-layer → increase robust/permeability barrier
- capsule/slime → barrier against antibacterials/dessication-phagocyte protection
what is the extracellular polysaccharide in
(1) pseudomonas aueriginosa
(2) leuconostoc mesateronides
- alginate
- dextran
what is the function of dextran
provides protection against external environment
enhances adhesion to solid surfaces
how do bacteria divide and grow?
most bacteria reproduce by binary fission
bacterial growth: change in population rather than size or mass
what is binary fission?
division into two identical daughter cells
what are the growth requirements for bacteria?
- warmth
- moist (water)
- proteins
- neutral or slightly acidic pH
- oxygen
what is microbial enumeration test?
quantative test that determines the total aerobic microbial count and total yeast and mold count present in test product
what are the methods available for microorganism enumeration?
- direct
- indirect
- viable
- total cell count
-
RMM:
- growth based
- direct measurement
- cell component analysis
what bacterial classes are there
- spherical (cocci)
- rod (bacilli)
- spiral (spirilla)
- coma (vibrois)
- corkscrew (spirochaetes)
why is bacterial identification important
because it is essential for correct diagnosis and treatment and trace back of disease outbreaks
what are some traditional and modern identification methods?
traditionals:
- cultivation (growth requirement)
- cultivation (selective agar)
- biochemical profiling
New/rapid:
- serological testing
- nucleic acid techniques
- MALDI TOF
draw a bacterial spore structure
how do sporulation and germination occur?
Spore is metabolically dormant structure produced during unfavorable condition by the process called sporulation. Sporulation occur during late log phase or early stationary phase. Under favorable condition spores germinate to give vegetative cell.
why are spores resistant to antimicrobials?
because they are highly dehydrated with no metabolic activity and their constituents of small acid soluble proteins dipicolinic acid and their multilayered structure
true or false
most spore forming bacteria are gram positive
true
define sterilization
process that kills all microorganisms including spores
which antibiotics are most likely to cause c.diff?
broad spectrum antibiotics like: cephalosporins/fluoroquinolones/ampicillin/amoxicillin/clindamycin
explain the cell cycle of chlamydia
- they alternate between infectious extracellular elementary body and reticulate body
- elementary bodies enter mucosal cells and differentiate to reticulate bodies in membrane bound compartment
- replication occurs, reticulate bodies redifferentiate into elementary bodies and released from host cell to infect other cells
what are the features of mycobacteria?
- hydrophobic cell wall, peptidoglycan linked to arabinogalactan esterfied to mycolic acid
- lipids 25% of dry weight
- mycolic acid, high molecular weight (3 hydroxy fatty acid)
- cord factor, parallel alignment of rows of bacilli
what treatments are available for TB
- isoniazid
- rifampicin
- pyrazinamide
- ethambutol
what are the common routes of infection?
- direct contact
- fomites
- aerosols
- oral
- vector borne
what is the normal flora?
microbes that are both helpful and potentially harmful occupying the a habitat (human)
what is a virulence factor?
microbial product that contributes to virulence
what is virulence?
intensity of pathogenicity of an organism
what are toxins?
substance of organisms that damage the host
what is an opportunistic pathogen?
organism that becomes pathogenic following a perturbation to a host / disruption of microflora
what is the difference between endotoxin and exotoxins?
endotoxins are toxic at high doses whereas exotoxins are can be extremely toxic at low doses.
endotoxins are released when bacterial cell dies
exotoxins produced during growth/division
what exotoxins are there?
neurotoxins
enterotoxins
cytotoxins
what is the toxic molecule of gram negative?
lipopolysaccharide molecule (Lipid A)
what’s the difference between DNA and RNA
what’s the difference between DNA polymerase and RNA polymerase
what factors affect antimicrobial treatment?
- bacterial status (resistance/biofilm/susceptibility)
- antimicrobial concentration and subinhibitory concentration
- host factors (serum effect/gut impact)
what are mycoses?
infections caused by fungus invading tissues and causing, superficial/subcutaneuous/systemic infections
where is candida present in the normal flora?
mouth
skin
intestine
draw the structure of a yeast cell
draw a yeast/fungi cell wall
how do yeast cells reproduce?
budding, whereby mother cell grows a protrusion (bud) until it’s the same size as the mother cell and splits from it
what antifungal drugs are there?
polyene: nyastatin + amphoterecin B
azole: itraconazole + ketoconazole
echinocandins: caspofungin/micafungin/anudiulafungin
synthetic: flucytosine
what are dermatomycoses?
fungal skin, hair, or nail infections by dermatophytes (ringworm)
what is aspergillosis?
fungal infection caused by aspergillus a common mold that lives both indoors and outdoors
describe the structure if mold and draw it
long branched thread-like filaments of hyphae that form mycelium
explain how mold reproduces sexually and asexually
molds reproduce sexually when they are starved, in which 4 haploid cells fuse into two and further into one (increase genetic diversity/survival)
they reproduce asexually when there’s plentiful food supply, producing 2 identical daughter diploid cells
give examples of viruses that use the following transmission means
direct contact
airborne
food/water
arthropod
direct contact → aids/hiv/hsv/hpv/leukemia/hepatitis b/c
airborne → chickenpox/influenza/measles/mumps/rubella/corona
food/water → gastroenteritis/norovirus/hepatitis A/poliomyelitis
arthropod → yellow fever
describe the basic structure of viruses
nucleic acid covered by capsid forming the nucleocapsid, with an envelope covering it along with viral receptors
what are the general steps of viral replication?
- attachment and penetration
- macromolecular synthesis
- assembly of progeny virions and release from host cell
describe structure of influenza
spherical with an outer lipid membrane (envelope) derived from host cell
what are the spike like protrusions on influenza virus
hemagglutinin (HA) and neuraminidase (NA)
what is the difference in antigenic drift and antigenic shift?
antigenic drift: two virus strains infect the same cell and mix during assembly of new viruses e.g. h3n2+h5n1=h5n2
antigenic drift: small changes in the virus over a period of time, producing new strains not recognized by immune system and are difficult to treat/vaccinate
how does influenza replicate inside host cell
influenza is a single stranded negative sense RNA virus, they have genomes which consist of more than 1 RNA viruses, transcription results in unique mRNA for each protein rather than a single polycistemic mRNA
define reassortment
process by which influenza viruses swap gene segments
how do herpes viruses replicate
herpes viruses are DNA containing viruses, which means they make mRNA using strategies similar to host cell replication, in which DNA is transcribed into mRNA in the host cell nucleus with host cell enzymes resulting in early and late transcripts that encode for structural proteins and those required for replication
what is herpes latent and productive infection?
productive infection: Following primary infection, the virus replicates productively within mucosal epithelial cells and enters sensory neurones via nerve termini
latent infection: e virus is then transported to neuronal cell bodies where latency can be established (it can reactivate and generate new virus progeny when transported back to periphery)
explain how herpes viruses reactivate
- initiation of viral lytic gene expression
- newly formed capsids are transported to axonal termini
- infectious virus released from axon and infects epithelial cell resulting in recurrent infection and virus shedding
what type of viruses are corona viruses
single stranded positive sense RNA
what enzymes does corona use in replication
RNA dependent RNA polymerase
what causes RNA-RNA recombination in corona
high intrinsic error rate, introducing multiple nucleotide changes, jump across templates
what mediates RNA proofreading
viral RNA exonuclease
what accounts for the highly diverse populations in viruses like corona?
the combination of RNA recombination due to high polymerase error and regulated replication fidelity favors the generation of recombinant and highly diverse viruses
how is SARS-COV-2 transmitted?
close contact
what is viral shedding?
release of virus progeny after assembly in host cell
what is SARS and what are the subtypes?
it stands for severe acute respiratory syndrome (SARS) that is a viral respiratory disease caused by coronaviruses
what type of virus is corona?
enveloped, positive sense RNA virus
how do antivirals affect viral processes in HIV?
zidovudine, is a reverse transcriptase inhibitors, It inhibits the activity of HIV-1 reverse transcriptase (RT) via DNA chain termination after incorporation of the nucleotide analogue. It competes with the natural substrate dGTP and incorporates itself into viral DNA.
how does HIV replicate?
uses CD4+ cells to replicate, The retroviruses, such as HIV, contain single-stranded positive-sense RNA but employ a unique replicative strategy using a DNA intermediate. Viral positive-sense RNA serves as a template for a virion-associated RNA-dependent DNA polymerase (reverse transcriptase). The DNA is then integrated into host chromosomal DNA, where it resides for the life of the cell. Transcription of the integrated viral DNA, like transcription of host cell genes, is carried out by host cell DNA-dependent RNA polymerases
what is HIV and AIDS?
HIV is a retrovirus that primarily infects CD4+ cells, macrophages, and dendritic cells
aids: acquired immunodeficiency syndrome that describes life threatening infections occurring due to damaged immune system caused by HIV
what is the CD4+ count of AIDS
below 200 cells per microlitre
viruses are mainly diagnosed by symptoms and clinical manifestations, what tests can be done to confirm diagnosis?
direct/indirect: isolation (immunofluoroescence)/ antigens/antibodies/PCR
biological specimens: nasopharynx swab/throat swab/rectal swab/eye swab/ lesion swab
what is malaria
unicellular, eukaryotic, heterotrophic microorganism that are sometimes parasitic depending on the life stage found in aqueous environments and they are transmitted via arthropod vectors
define helminths
parasitic worms such as flukes and tapeworm
what diseases are caused by helminths?
schistosomiasis
lymphatic filariasis
cysticercosis
onchocerciases
what is the role of microbiome?
metabolism → biochemical pathway for non digestible foods (cellulose/gum/hemicellulose/pectins). synthesize vitamins k and b12 and develop caucum
immune development: produce antimicrobials (fatty acids/peroxides) and compete for nutrient sites in sites of attachment in the gut preventing colonization
gut-brain-axis → stress influences microbiota composition and integrity of gut epithelium
what diseases result from the disruption of normal microflora?
inflammatory bowel syndrome
obesity/diabetes 2
atopic eczema and allergies
what are probiotics
microorganisms believed to provide health benefits when consumed
what are the sources of contamination?
- contaminated manure
- irrigation water
- soil
- livestock/wildlife
how can you minimize, control or eliminate contamination?
water → chemical treatment NaCl/membrane filtration/UV irradiation 250nm/heating 80c
operator → gloves/good hygiene/cover when sneezing
buildings → good ventilation/disinfectant/filtration/floor cleaning/avoid drainage in manufactures/dusting
packages → maintain integrity (shelf-life)/safe delivery
equipment → sterilizaition/disinfection/disposable (single use)
air → filtration (HEPA)/chemical disinfection/UV radiation
what are the benefits of microbes
- transform heavy metals like mercury to non toxic form
- petroleum biodegradation
- xenobiotic degradation
how have microorganisms been harnessed for various purposes?
- leuconostoc bacteria can produce dextran from sucrose which is an antithrombotic that improves tissue function
- clostridium botilinum produces botilinum toxin that is used in minute amounts in the cosmetic industry to prevent wrinkles and to treat dystonia
- bacillus sphaericus produce 51 & 42 kDA which are toxic to larvae and used in waters where larvae develop
Describe the stereochemistry of amino acids
Almost all amino acids contain a chiral centre on the alpha carbon. All naturally occurring amino acids have L-stereochemistry, i.e. they have the same configuration as the reference compound glyceraldehyde. D-amino acids are very rare, and are the product of biosynthesis
Explain what is unusual about the stereochemistry of glycine. Explain your answer
Glycine has no chiral centre and therefore cannot exist in L/D-forms. The alpha carbon does not have four non-identical groups attached, two are hydrogen (i.e. identical
Explain how i) acidic and ii) basic conditions would affect the amino acids shown
Acidic conditions will protonate the basic side chain of Lys, becoming positively charged. Basic conditions will deprotonate the acidic carboxylic acid group, becoming negatively charged. (You could also, or might be asked, to draw the resulting structures
Provide a concise definition of a peptide
A small protein containing 50 or less amino acid residues
Briefly describe the nomenclature of peptides
Peptides should be named, using three letter or single letter amino acid abbreviations starting from the N-terminal residue and listing sequentially to the C-terminal. Abbreviations separated by dashes.
Consider the decapeptide (below) and answer the following questions: Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
a) Name the N-terminal amino acid.
b) Name the C-terminal amino acid.
a. Lysine
b. Aspartic acid
Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
State the side chain property of each amino acid in the peptide
Lys – basic
Ala, Val, Leu and Ile – hydrophobic
Ser – polar; Asp – Acidic
Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
How you would expect this peptide to fold in an aqueous solution? Fully explain your answer and include a rough sketch of this conformation.
in an aqueous environment, hydrophobic residues e.g. Ala, Val etc would be folded away from water into the interior of the protein. Hydrophilic residues, e.g. Ser, would face the solvent. Charged side chains would form an interaction where possible.
Lys-Ala-Val-Ala-Leu-Ser-Ile-Leu-Val-Asp
Would you predict this peptide to be water soluble? Briefly explain your answer
Will have some water solubility, although mostly non-polar amino acids there are three polar aa’s, two of which form a salt. OR – will not be soluble in water as 7 non-polar aa’s versus 3 polar.
describe the structure of a globular protein
Compact (tightly folded), roughly spherical, structurally complex, comprised of many elements of secondary structure, e.g. alpha helix, beta sheet, often clearly defined active site / cleft, internal bonding to maintain structure, e.g. disulfide bridges
give an example of a globular protein
trypsin (all enzymes)
Describe the general properties of a globular protein.
Hydrophobic interior, hydrophilic exterior, water soluble, often function as catalysts
Describe how the three-dimensional structure of a globular protein is maintained.
ionic interactions, hydrogen bonding, hydrophobic interactions, covalent crosslinks
true or false
the alpha helix is a double helix
false
The alpha helix is a single peptide backbone coiled around itself and stabilised by intra-strand H-bonds. [By contrast, DNA is an example of a double helix – two chains stabilised by inter-strand H-bonds]
true or false
The native conformation is the biologically active form of a protein.
true
All proteins fold spontaneously into a conformation that is biological active
true or false
The peptide bond usually adopts a trans conformation
true
Cis-amide bonds force unfavourable steric interactions between aa side chains and are not commonly found in proteins
true or false
parallel beta sheets are more stable than antiparallel beta sheets
false
Anti-parallel beta sheets are more stable – the network of inter-strand H-bonds are better aligned and more stable in the anti-parallel type.
what is Native conformation
Proteins do not exist as a linear conformation of amino acids (the primary sequence) they fold very specifically into a specific conformation called the native conformations. This is generally the biologically active form of the protein
what is alpha Helix
. Alpha helix important form of secondary protein structure. Single polypeptide strand coiled in a tight helix excluding water from the centre. + + Describe properties and H-bonding network etc. Some proteins composed exclusively of a-helix, usually as coils of coils, e.g. keratin, collagen. Also common in membrane spanning receptors
what is a Non-essential amino acid.
An amino acid that can be biosynthesized with the body and therefore is not essential in the diet. E.g. Ala, Gly, Pro, Ser etc. It requires energy and raw materials to synthesize aa’s so in practice these are obtained from diet whenever possible
what is a Cyclic peptide
A polypeptide joined via an amide (peptide) bond between the N and C terminal amino acids creating a continuous cyclic peptide backbone. Have pharmaceutical use. E.g. ciclosporin, a microbial cyclic peptide that contains non-coding biosynthesized amino acids. When non-amino acid groups are incorporated known as a pseudo-peptide
Very briefly describe how enzymes function as catalysts
…by lowering the activation energy barrier to the reaction. Achieved by precise orientation of the substrate in the active site in a reactive conformation and provide missing functional groups or cofactors for the reaction. Enzymes provide the reaction ‘template’.
Briefly describe how enzymes are named and classified. Illustrate your answer with suitable examples
Two methods, trivial and systematic. Trivial – name associated with the function or substrate (or both) is suffixed with –ase. E.g. L-dopa decarboxylase or DNA polymerase. Systematic system (enzyme commission: EC) assigns a unique serial number comprised of 4 digits. First digit is one of the six classes (list them) followed by two sets of sub classes and finally the unique identifier, e.g. alcohol dehydrogenase = EC1.1.1.1.
Many enzymes require cofactors for their biological function. Discuss this statement using alcohol dehydrogenase and another enzyme of your choice to illustrate your answer.
The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Alcohol dehydrogenase uses two co-factors, a zinc ion and a NAD+ coenzyme. The zinc aligns the substrate in the active site to the –OH group. The NAD+ contains a functional group that accepts a proton (i.e. dehydrogenation). Could also include a sketch? Another example could be L-Dopa decarboxylase. The enzyme uses a co-enzyme (pyridoxal phosphate/vitB6) to facilitate the removal of a carboxylic acid. The co-enzyme contains an aldehyde functional group – not found in amino acids – to form an intermediate (imine) with the substrate etc etc
Briefly discuss the importance of metals in protein function. Give one example of a protein that requires a metal atom to function
Proteins containing metal ions are known as metalloproteins or metalloenzymes if they have a catalytic function. The 20 amino acids that occur naturally in proteins have limited functional groups / chemistry in their side chains. Co-factors, which can be metal ions or organic molecules (co-enzymes) supply this chemistry. Metals are important in transport proteins (e.g. haemoglobin, Fe required to bind, store then release O2, four Fe atoms held in 4 prosthetic haem groups etc etc). Alcohol dehydrogenase and Zn etc etc
what are the products of the following:
glycolysis
pyruvate → acetyl coa
krebs cycle
glycolysis: 2 pyruvate + 2ATP +2 NADH
pyruvate → acetyl coa: 2 NADH per glucose
krebs: coa to co2+ 2GTP + 6NADH + 2 FADH2
define fatty acid
occur as esters in natural fats and oils and FFA in blood
what’s the difference between saturated and unsaturated fatty acid?
saturated: no double bonds in acyl chains, end in anoic e.g butyric acid
unsaturated: 1 to several double bonds in acyl chain, end in enoic e.g. oleic acid
what’s the difference between fat and oil
fats have more/all available bonding sites TAKEN UP by Hydrogen (saturated). whereas, oils have fewer hydrogens on the account of double bonds (unsaturated) they are also liquid at room temperature
what is a liposome?
a minute spherical sac of phospholipid molecules enclosing a water droplet, especially as formed artificially to carry drugs or other substances into the tissues.
what is a micelle?
ggregate of surfactant phospholipid molecules dispersed in a liquid, forming a colloidal suspension.
what is the basic structure of a phospholipid
glycerol
phosphate
fatty acid side chain
briefly describe the following and their funtion
cytoplasm/cytosol/mitochondria/peroxisomes/nucleus/lysosomes/ER/Golgi
cytoplasm → contains all cell organelles except nucleus
cytosol → densely packed aqueous gel, protein synthesis
mitochondria → cellular respiration/apoprosis/oxidative phosphorylation
lysosomes → cellular digestion/enzyme function site
peroxisomes → site of oxygen utilization
nucleus → DNA/RNA synthesis
ER → lipid synthesis/protein distribution
Golgi → modification/sorting/packaging of proteins + delivery and secretion
lysosomes → cellular digestion
is oxygen needed to produce ATP
Without oxygen, organisms can split glucose into just two molecules of pyruvate. This releases only enough energy to make two ATP molecules. With oxygen, organisms can break down glucose all the way to carbon dioxide. This releases enough energy to produce up to 38 ATP molecules
